Microbial and biogeochemical changes following soil disturbance are immediate and may persist for decades to centuries.  Changes have been documented in widely different ecosystems following tillage, mining, road construction, plant invasions, and other forms of soil disturbance, and include altered microbial community structure and enzyme activities, accelerated soil nutrient turnover, and increased trace gas emissions.  These changes add to a substantive environmental burden: trace gas increases have contributed substantially to elevated concentrations of atmospheric greenhouse gases; soil organic matter losses have decreased soil productivity and increased the need for external nutrient inputs; and accelerated rates of soil erosion and N leaching have reduced surface- and groundwater quality.  A variety of environmental modifications underlie these changes, almost all of which can be related to soil disaggregation.  We present here a conceptual model, based on research into tillage effects on a previously uncultivated soil in southwest Michigan, describing the controlling influence of aggregates on short-term microbial and biogeochemical responses to disturbance.  We show that aggregates can decline by more than 50% following initial disturbance and that this sets into motion a dramatic cascade of changes (a “disaggregation cascade”) in organic matter availability, activities of C- and N-cycle enzymes, soil nutrient cycling, and soil surface-atmosphere exchanges of CO₂, N₂O, and CH₄.  The disaggregation cascade explains the potentially high risk of soil organic matter loss following tillage of set-aside lands (e.g. Conservation Reserve Program land), and also the mechanisms underlying immediate responses to disturbance associated with mining, road construction, and other land-use changes that destroy soil structure.